calibration: show application timestamp in table

changelog.md

@@ -9,7 +9,8 @@
 * Calibration results and parameters are now accessible via properties which are listed when items are printed. See [calibration results](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.force_calibration.power_spectrum_calibration.CalibrationResults.html) and [calibration item](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.calibration.ForceCalibrationItem.html) API documentation for more information.
 * Added `applied_at` property to a [calibration item](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.calibration.ForceCalibrationItem.html) obtained from a force slice. This property returns the timestamp in nanoseconds at which the force calibration was applied.
 * Added improved printing of calibration items under `channel.calibration` providing a more convenient overview of the items associated with a `Slice`.
-* Added parameter `titles` to customize title of each subplot in `[`Kymo.plot_with_channels()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.kymo.Kymo.html#lumicks.pylake.kymo.Kymo.plot_with_channels).
+* Added improved printing of calibrations performed with `Pylake`.
+* Added parameter `titles` to customize title of each subplot in [`Kymo.plot_with_channels()`](https://lumicks-pylake.readthedocs.io/en/latest/_api/lumicks.pylake.kymo.Kymo.html#lumicks.pylake.kymo.Kymo.plot_with_channels).
 
 ## v1.5.1 | 2024-06-03
 

lumicks/pylake/calibration.py

@@ -1,4 +1,5 @@
 import re
+import datetime
 from functools import wraps
 from collections import UserDict
 
@@ -49,14 +50,6 @@ def _sensor_type(self):
         else:
             return "unknown sensor"
 
-    @property
-    def kind(self):
-        kind = self.data.get("Kind", "Unknown")
-        if kind == "Full calibration":
-            return "Active calibration" if self.active_calibration else "Passive calibration"
-        else:
-            return kind
-
     @_verify_full
     def power_spectrum_params(self):
         """Returns parameters with which the power spectrum was calculated
@@ -199,27 +192,6 @@ def number_of_samples(self):
         """Number of fitted samples (-)."""
         return self.data.get("Number of samples")
 
-    @property
-    def active_calibration(self):
-        """Returns whether it was an active calibration or not
-
-        Calibrations based on active calibration are less sensitive to assumptions about the
-        bead diameter, viscosity, distance of the bead to the flow cell surface and temperature.
-        During active calibration, the trap or nano-stage is oscillated sinusoidally. These
-        oscillations result in a driving peak in the force spectrum. Using power spectral analysis,
-        the force can then be calibrated without prior knowledge of the drag coefficient.
-
-        While this results in improved accuracy, it may lead to an increase in the variability of
-        results.
-
-        .. note::
-
-            When active calibration is performed using two beads, correction factors must be
-            computed which account for the reduced flow field that forms around the beads due to
-            the presence of a second bead.
-        """
-        return self.data.get("driving_frequency (Hz)") is not None
-
     @property
     def num_points_per_block(self):
         """Number of points per block used for spectral down-sampling"""
@@ -367,11 +339,15 @@ def from_field(hdf5, force_channel, time_field="Stop time (ns)") -> "ForceCalibr
 
         return ForceCalibration(time_field=time_field, items=items)
 
-    def print_summary(self, tablefmt):
+    def _print_summary(self, tablefmt):
+        def format_timestamp(timestamp):
+            return datetime.datetime.fromtimestamp(int(timestamp)).strftime("%x %X")
+
         return tabulate(
             (
                 (
                     idx,
+                    format_timestamp(item.applied_at / 1e9) if item.applied_at else "-",
                     item.kind,
                     f"{item.stiffness:.2f}" if item.stiffness else "N/A",
                     f"{item.force_sensitivity:.2f}" if item.force_sensitivity else "N/A",
@@ -389,7 +365,8 @@ def print_summary(self, tablefmt):
             ),
             tablefmt=tablefmt,
             headers=(
-                "Index",
+                "#",
+                "Applied at",
                 "Kind",
                 "Stiffness (pN/nm)",
                 "Force sens. (pN/V)",
@@ -401,10 +378,10 @@ def print_summary(self, tablefmt):
         )
 
     def _repr_html_(self):
-        return self.print_summary(tablefmt="html")
+        return self._print_summary(tablefmt="html")
 
     def __str__(self):
-        return self.print_summary(tablefmt="text")
+        return self._print_summary(tablefmt="text")
 
     @staticmethod
     def from_dataset(hdf5, n, xy, time_field="Stop time (ns)") -> "ForceCalibration":

lumicks/pylake/force_calibration/power_spectrum_calibration.py

@@ -581,6 +581,35 @@ def offset(self):
         """Force offset (pN)"""
         return self._get_parameter("NA", "Offset")
 
+    @property
+    def active_calibration(self):
+        """Returns whether it was an active calibration or not
+
+        Calibrations based on active calibration are less sensitive to assumptions about the
+        bead diameter, viscosity, distance of the bead to the flow cell surface and temperature.
+        During active calibration, the trap or nano-stage is oscillated sinusoidally. These
+        oscillations result in a driving peak in the force spectrum. Using power spectral analysis,
+        the force can then be calibrated without prior knowledge of the drag coefficient.
+
+        While this results in improved accuracy, it may lead to an increase in the variability of
+        results.
+
+        .. note::
+
+            When active calibration is performed using two beads, correction factors must be
+            computed which account for the reduced flow field that forms around the beads due to
+            the presence of a second bead.
+        """
+        return self.driving_frequency is not None
+
+    @property
+    def kind(self):
+        kind = self._get_parameter("Kind", "Kind")
+        if kind == "Full calibration":
+            return "Active" if self.active_calibration else "Passive"
+        else:
+            return kind if kind is not None else "Unknown"
+
 
 class CalibrationResults(CalibrationPropertiesMixin):
     """Power spectrum calibration results.
@@ -653,15 +682,6 @@ def _get_parameter(self, pylake_key, _):
         if pylake_key in self:
             return self[pylake_key].value
 
-    @property
-    def kind(self):
-        """Type of calibration performed"""
-        return (
-            "active calibration"
-            if self.model.__class__.__name__ == "ActiveCalibrationModel"
-            else "passive calibration"
-        )
-
     @property
     def _fitted_diode(self):
         """Diode parameters were fitted"""
@@ -1006,6 +1026,7 @@ def fit_power_spectrum(
                 "Chi squared per degree of freedom", chi_squared_per_deg, ""
             ),
             "backing": CalibrationParameter("Statistical backing", backing, "%"),
+            "Kind": CalibrationParameter("Calibration type", "Full calibration", "-"),
         },
         params={
             **model.calibration_parameters(),

lumicks/pylake/force_calibration/tests/test_active_calibration.py

@@ -97,6 +97,9 @@ def test_integration_active_calibration(
     np.testing.assert_allclose(fit["Viscosity"].value, viscosity)
     np.testing.assert_allclose(fit["num_windows"].value, 5)
 
+    assert fit.active_calibration
+    assert fit.kind == "Active"
+
     np.testing.assert_allclose(
         fit["driving_amplitude"].value, driving_sinusoid[0] * 1e-3, rtol=1e-5
     )

lumicks/pylake/force_calibration/tests/test_hydro.py

@@ -380,6 +380,8 @@ def test_integration_passive_calibration_hydrodynamics(integration_test_paramete
     assert not fit.transferred_lateral_drag_coefficient  # Only relevant for axial
     assert fit.fit_range == (100, 23000)
     assert fit.excluded_ranges == []
+    assert not fit.active_calibration
+    assert fit.kind == "Passive"
 
 
 def test_integration_active_calibration_hydrodynamics_bulk(integration_test_parameters):

lumicks/pylake/tests/test_file/test_file.py

@@ -75,21 +75,35 @@ def test_redirect_list(h5_file):
         assert f["Point Scan"]["PointScan1"].start == np.int64(20e9)
 
 
-def test_calibration_str(h5_file):
+def test_calibration_str(h5_file, monkeypatch):
+    # Representation of time is timezone and locale dependent, hence we monkeypatch it
+    class FakeDateTime:
+        @classmethod
+        def fromtimestamp(cls, timestamp, *args, **kwargs):
+            """Inject a timezone"""
+            return FakeDateTime()
+
+        def strftime(self, str_format):
+            return str_format
+
     f = pylake.File.from_h5py(h5_file)
     if f.format_version == 2:
-        print("")
-        print(str(f.force1x.calibration))
-        assert str(f.force1x.calibration) == dedent(
-            (
-                """\
-                  Index  Kind                 Stiffness (pN/nm)    Force sens. (pN/V)    Disp. sens. (µm/V)    Hydro    Surface    Data?
-                -------  -------------------  -------------------  --------------------  --------------------  -------  ---------  -------
-                      0  Unknown              N/A                  N/A                   N/A                   False    False      False
-                      1  Reset offset         1.05                 504.43                4.57                  False    True       False
-                      2  Passive calibration  1.05                 504.43                4.57                  False    False      True"""
+        with monkeypatch.context() as m:
+            m.setattr(
+                "lumicks.pylake.calibration.datetime.datetime",
+                FakeDateTime,
+            )
+
+            assert str(f.force1x.calibration) == dedent(
+                (
+                    """\
+                      #  Applied at    Kind          Stiffness (pN/nm)    Force sens. (pN/V)    Disp. sens. (µm/V)    Hydro    Surface    Data?
+                    ---  ------------  ------------  -------------------  --------------------  --------------------  -------  ---------  -------
+                      0  -             Unknown       N/A                  N/A                   N/A                   False    False      False
+                      1  %x %X         Reset offset  1.05                 504.43                4.57                  False    True       False
+                      2  %x %X         Passive       1.05                 504.43                4.57                  False    False      True"""
+                )
             )
-        )
 
 
 def test_repr_and_str(h5_file):